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| #acl AdminGroup:read,write,delete,revert KoenVanLeemput:read,write AdrianKCLee:read,write All: '''Deadlines''' *December 29th - notify wait-listers of status; notify registrants of payment due date *January 9th - tutorials/wikis completed; release new stable freesurfer *January 9th - deadline for payment; mail out pre-packets *January 13th - data must be on all laptops *January 16th - run through complete *January ? - paper materials ready for printing Pre-packets: *Unix tutorial *Wiki suggested links *Stream Page *Papers |
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| || 8:00 - 9:00 || Course Registration || sign-in || staff || binders with slides, acquisition parameters? relevant papers? nametags, coffee || | || 8:00 - 9:00 || Course Registration || sign-in || staff || glossary link for here and printout for binders || |
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| || 10:00 - 10:30 || Reliability/Validation of !FreeSurfer || talk || David Salat || || | || 10:00 - 10:30 || Reliability/Validation of !FreeSurfer || talk || David Salat || Nick give David slide on longitudinal analysis || |
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| || 9:45 - 10:45 || ROI Analysis || tutorial || staff || seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David) || | || 9:45 - 10:45 || [[FsTutorial/AnatomicalROI|ROI Analysis]] || tutorial || staff || seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David) || |
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| || 11:00 - 11:15 || [[attachment:freesurfer.failure_modes.2008.ppt|Failure Modes]] || talk || Bruce Fischl|| Bruce will give intro to 'scare' tutorial|| | || 11:00 - 11:15 || [[attachment:freesurfer.failure_modes.2009.ppt|Failure Modes]] || talk || Bruce Fischl|| Bruce will give intro to 'scare' tutorial|| |
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| || 4:30 - 5:00 || [[attachment:freesurfer.inferring_architectonics.2008.ppt|Inferring architectonic boundaries from in-vivo MRI]] || talk || Bruce Fischl || || || 5:00 - 5:20 || Combined Volume and Surface Registration || talk || Lilla Zollei || maybe some children stuff (my pet goat)|| |
|| 4:30 - 5:00 || [[attachment:freesurfer.inferring_architectonics.2009.ppt|Inferring architectonic boundaries from in-vivo MRI]] || talk || Bruce Fischl || all talks on Bruce's laptop || || 5:00 - 5:20 || [[attachment:CVS-lzollei.ppt|Combined Volume and Surface Registration]] || talk || Lilla Zollei || || |
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| || 5:40 - 6:00 || Automated segmentation of hippocampal subfields || talk || Koen Van Leemput || || | || 5:40 - 6:00 || [attachment:HippocampalSubfields-Koen.ppt|Automated segmentation of hippocampal subfields]] || talk || Koen Van Leemput || || |
Tuesday, January 20th - Introduction to FreeSurfer
Time |
Title |
Type |
Lecturer |
To Do/Topics covered |
8:00 - 9:00 |
Course Registration |
sign-in |
staff |
glossary link for here and printout for binders |
8:00 - 8:30 |
optional - Unix Tutorial for FreeSurfer 1. Surrey, 2. O'Reilly |
tutorial |
Allison Stevens |
|
9:00 - 9:20 |
talk |
Bruce Fischl |
David making flowchart of overview |
|
9:20 - 10:00 |
FreeSurfer Applications |
talk |
David Salat |
|
10:00 - 10:30 |
Reliability/Validation of FreeSurfer |
talk |
David Salat |
Nick give David slide on longitudinal analysis |
10:30 - 10:45 |
break |
|
|
|
10:45 - 11:45 |
talk |
Doug Greve |
example of good data; update on the typical failure modes (Sita editing tutorial); detail on directories (Allison has a slide); aseg stats surface based vs. voxel based |
|
10:45 - 11:00 |
Tkmedit/Tksurfer demonstration |
demo |
Doug Greve |
|
11:00 - 12:30 |
tutorial |
staff |
jacobian? |
|
12:30 - 1:15 |
lunch |
|
|
|
1:15 - 2:30 |
talk |
Doug Greve |
mapping labels; loading functional on surface and in volume; Brodmann's areas |
|
2:30 - 2:45 |
QDEC demonstration |
demo |
Nick Schmansky |
|
2:45 - 3:00 |
break |
|
|
|
3:00 - 4:00 |
tutorial |
staff |
|
|
4:00 - 5:00 |
tutorial |
staff |
find old tutorial and spruce up |
|
5:00 - |
optional - FreeSurfer Installation on Personal Laptops |
tutorial |
Nick Schmansky |
get tarball on external usb harddisks; router; announce versions we will support |
5:00 - |
optional - Start Processing Your Own Data |
tutorial |
Allison Stevens |
|
Wednesday, January 21st - Working with Various Data Types
Time |
Title |
Type |
Lecturer |
To Do/Topics covered |
9:00 - 9:45 |
talk |
Doug Greve |
Extracting ROI measures from anatomial data (stats files). Exporting ROI stats; ICV; Creating your own labels; mapping labels between subjects; how to draw labels and how to get stats from labels (tutorial); aseg editing in tkmedit in wiki; parcellation edits? how divide label in thirds; CMA papers; your own atlas; thickness |
|
9:45 - 10:45 |
tutorial |
staff |
seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David) |
|
10:45 - 11:00 |
break |
|
|
|
11:00 - 11:15 |
talk |
Bruce Fischl |
Bruce will give intro to 'scare' tutorial |
|
11:15 - 12:15 |
tutorial |
staff |
'scare' tutorial, defect_seg, bugr |
|
12:15 - 1:00 |
lunch |
|
|
|
1:00 - 2:15 |
talk |
Doug Greve |
Cross-modal registration; Application to fMRI: HRF and activation maps in ROI and surface. DTI: integration with WM Parc. tkregister2 tutorial (Doug); bbregister wiki (Doug) |
|
2:15 - 3:15 |
tutorial |
staff |
David dt_recon wiki; label2label; ask someone for SPM directions; wmparc (add to wiki); how to load DTI data (add to wiki) |
|
3:15 - 3:30 |
break |
|
|
|
3:30 - 4:30 |
Question and Answer Session |
talk |
staff |
exam questions |
4:30 - 6:00 |
Future Directions of FreeSurfer: |
|
|
|
4:30 - 5:00 |
talk |
Bruce Fischl |
all talks on Bruce's laptop |
|
5:00 - 5:20 |
talk |
Lilla Zollei |
|
|
5:20 - 5:40 |
TRActs Constrained on UnderLying Anatomy (TRACULA) |
talk |
Anastasia Yendiki |
|
5:40 - 6:00 |
[attachment:HippocampalSubfields-Koen.ppt|Automated segmentation of hippocampal subfields]] |
talk |
Koen Van Leemput |
|